Issue with Phame tree topology

[ChloeAmbroset]

Hello,

I have an Issue with Phame that is difficult to overcome. We succed to solve the issues with Samtools but when I run the tools, I have phylogenetical trees with no lenght branch. Phame tells me that 0 informative sites are considered !!
Alignment has 70 sequences with 889513 columns, 4 distinct patterns
0 parsimony-informative, 0 singleton sites, 889513 constant sites

When I open the .issue file, it starts with
Smartmatch is experimental at /shared/ifbstor1/projects/mbvdiv/src/PhaME/src/../lib/misc_funcs.pm line 26.
Error running nc1 nucmer --maxmatch -p Mbv_JP_KG4397_Mbv_CH_JF4278_corrected stats/Mbv_JP_KG4397_norepeats.fna stats/Mbv_CH_JF4278_corrected_norepeats.fna 2>/dev/null.
and it keeps continue with my following references ...

How can I do to overcome these issues ?
Thank's a lot for your reply

Best regards

Chloé